Using genetic markers to orient the edges in quantitative trait networks: the NEO software.

BMC Systems Biology
Jason E AtenSteve Horvath

Abstract

Systems genetic studies have been used to identify genetic loci that affect transcript abundances and clinical traits such as body weight. The pairwise correlations between gene expression traits and/or clinical traits can be used to define undirected trait networks. Several authors have argued that genetic markers (e.g expression quantitative trait loci, eQTLs) can serve as causal anchors for orienting the edges of a trait network. The availability of hundreds of thousands of genetic markers poses new challenges: how to relate (anchor) traits to multiple genetic markers, how to score the genetic evidence in favor of an edge orientation, and how to weigh the information from multiple markers. We develop and implement Network Edge Orienting (NEO) methods and software that address the challenges of inferring unconfounded and directed gene networks from microarray-derived gene expression data by integrating mRNA levels with genetic marker data and Structural Equation Model (SEM) comparisons. The NEO software implements several manual and automatic methods for incorporating genetic information to anchor traits. The networks are oriented by considering each edge separately, thus reducing error propagation. To summarize the genetic e...Continue Reading

References

Nov 1, 1990·Epidemiology·S Greenland
Aug 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Xianghong ZhouWing Hung Wong
Nov 5, 2002·BMC Bioinformatics·Martin SteffenGeorge Church
Apr 12, 2003·International Journal of Epidemiology·George Davey Smith, Shah Ebrahim
Apr 13, 2004·International Journal of Epidemiology·Duncan C Thomas, David V Conti
Oct 14, 2004·Bioinformatics·Juliane Schäfer, Korbinian Strimmer
May 12, 2005·Statistics in Medicine·John R ThompsonRichard D Riley
Apr 15, 2006·Journal of Epidemiology and Community Health·George Davey Smith
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Bin Zhang, Steve Horvath
May 25, 2006·BMC Genomics·David C Kulp, Manjunatha Jagalur
Jul 11, 2006·Genome Research·Xia YangAldons J Lusis
Jul 20, 2006·PLoS Genetics·Renhua LiGary A Churchill
Aug 22, 2006·Plant Physiology·Hairong WeiAnn Loraine
Aug 29, 2006·PLoS Genetics·Anatole GhazalpourSteve Horvath
Sep 26, 2006·Canadian Journal of Physiology and Pharmacology·Catherine Mounier, Barry I Posner
Nov 9, 2006·Proceedings of the National Academy of Sciences of the United States of America·S HorvathP S Mischel
Nov 15, 2006·Proceedings of the National Academy of Sciences of the United States of America·Michael C OldhamDaniel H Geschwind
Apr 6, 2007·BMC Systems Biology·Florian GeierChristian Fleck
Jul 27, 2007·BMC Systems Biology·Arne B GjuvslandStig W Omholt
Jul 27, 2007·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Solveig K Sieberts, Eric E Schadt
Aug 2, 2007·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Tova F FullerSteve Horvath
Sep 26, 2007·BMC Systems Biology·Mark Müller-LinowMarc-Thorsten Hütt
Oct 18, 2007·BMC Bioinformatics·Jing ChenAnil G Jegga

❮ Previous
Next ❯

Citations

Jul 18, 2012·Current Osteoporosis Reports·Charles R Farber
Jul 29, 2009·Nature Reviews. Genetics·Vivian G Cheung, Richard S Spielman
Mar 24, 2010·Journal of Biopharmaceutical Statistics·Wei ZhaoSteve Hovarth
Jul 9, 2011·Bioinformatics·Andrea PinnaAlberto de la Fuente
Aug 4, 2009·Human Molecular Genetics·Luz D OrozcoAldons J Lusis
Feb 12, 2011·Genetics, Selection, Evolution : GSE·Guilherme J M RosaMartinho A Silva
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Mar 18, 2011·BMC Systems Biology·Christopher C ParkDesmond J Smith
Nov 27, 2008·Journal of Lipid Research·Sulin WuThomas A Drake
Dec 15, 2010·PLoS Computational Biology·Benjamin A Logsdon, Jason Mezey
May 30, 2013·PLoS Computational Biology·Xiaodong CaiGeorgios B Giannakis
Mar 4, 2014·PLoS Computational Biology·Lingxue Zhang, Seyoung Kim
Sep 17, 2010·PLoS Genetics·Michael InouyeLeena Peltonen
Feb 2, 2011·PLoS Genetics·Leopold PartsRichard Durbin
Jan 10, 2013·PLoS Genetics·Gina CalabreseCharles R Farber
Jan 5, 2013·Genetics·Elias Chaibub NetoBrian S Yandell
Jan 1, 2014·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Robert HitzemannShannon McWeeney
May 3, 2014·The Journal of Clinical Investigation·Larry D MesnerCharles R Farber
Apr 20, 2014·Current Cardiology Reports·Gad AbrahamMichael Inouye
Dec 11, 2013·Nucleic Acids Research·Chien-Hua PengWen-Ping Hsieh
May 13, 2014·Chromosoma·Yuichiro Itoh, Arthur P Arnold
Feb 2, 2016·Journal of Biomedical Informatics·Azam YazdaniEric Boerwinkle
Mar 19, 2013·Virus Research·Laurence JossetMichael G Katze
Feb 24, 2012·European Neuropsychopharmacology : the Journal of the European College of Neuropsychopharmacology·Sanghyeon KimMaree J Webster
Aug 3, 2011·Biochimica Et Biophysica Acta·Peter LangfelderMargarete Mehrabian
Oct 19, 2010·Trends in Genetics : TIG·Yang LiRitsert C Jansen
Mar 30, 2010·Seminars in Nephrology·Benjamin KellerMatthias Kretzler
Sep 5, 2008·Journal of Bone and Mineral Research : the Official Journal of the American Society for Bone and Mineral Research·Charles R FarberAldons J Lusis
Dec 24, 2010·Molecular Systems Biology·Michael InouyeLeena Peltonen
Apr 14, 2009·American Journal of Human Genetics·Jennifer A WebsterAmanda J Myers
Jul 8, 2015·Nature Reviews. Genetics·Neelroop N ParikshakDaniel H Geschwind

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Methods Mentioned

BETA
transgenic

Software Mentioned

LEO
R package sem
R
R sem
SingleMarker
Excel
sem R
NEO
NB
HiddenConfounder

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